Genetic Variant ADARB2:c.-5C>T (chr10-1737155-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018702.4(ADARB2):c.-5C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.538 in 1,605,374 control chromosomes in the GnomAD database, including 236,640 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.52 ( 21076 hom., cov: 33)

Exomes 𝑓: 0.54 ( 215564 hom. )

Consequence

ADARB2
NM_018702.4 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.00

Publications

12 publications found

Variant links:

Genes affected

ADARB2 (HGNC:227): (adenosine deaminase RNA specific B2 (inactive)) This gene encodes a member of the double-stranded RNA adenosine deaminase family of RNA-editing enzymes and may play a regulatory role in RNA editing. [provided by RefSeq, Jul 2008]

ADARB2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4 link	c.-5C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	ENST00000381312.6	NP_061172.1	Q9NS39-1
ADARB2	NM_018702.4 link	c.-5C>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000381312.6	NP_061172.1	Q9NS39-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6 link	c.-5C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	1	NM_018702.4	ENSP00000370713.1		Q9NS39-1
ADARB2	ENST00000381312.6 link	c.-5C>T		5_prime_UTR_variant	Exon 1 of 10	1	NM_018702.4	ENSP00000370713.1		Q9NS39-1

Frequencies

GnomAD3 genomes

AF:

0.521

AC:

79135

AN:

152018

Hom.:

21065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.511

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.549

GnomAD2 exomes

AF:

0.496

AC:

120948

AN:

243712

AF XY:

0.504

show subpopulations

Gnomad AFR exome

AF:

0.514

Gnomad AMR exome

AF:

0.437

Gnomad ASJ exome

AF:

0.577

Gnomad EAS exome

AF:

0.153

Gnomad FIN exome

AF:

0.488

Gnomad NFE exome

AF:

0.552

Gnomad OTH exome

AF:

0.528

GnomAD4 exome

AF:

0.540

AC:

784227

AN:

1453238

Hom.:

215564

Cov.:

AF XY:

0.541

AC XY:

391029

AN XY:

723330

show subpopulations

African (AFR)

AF:

0.509

AC:

17047

AN:

33462

American (AMR)

AF:

0.444

AC:

19837

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

15037

AN:

26120

East Asian (EAS)

AF:

0.163

AC:

6472

AN:

39686

South Asian (SAS)

AF:

0.531

AC:

45824

AN:

86250

European-Finnish (FIN)

AF:

0.484

AC:

21904

AN:

45254

Middle Eastern (MID)

AF:

0.544

AC:

3129

AN:

5748

European-Non Finnish (NFE)

AF:

0.561

AC:

623284

AN:

1111686

Other (OTH)

AF:

0.525

AC:

31693

AN:

60320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

19906

39812

59717

79623

99529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17368

34736

52104

69472

86840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.521

AC:

79188

AN:

152136

Hom.:

21076

Cov.:

AF XY:

0.514

AC XY:

38237

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.511

AC:

21222

AN:

41520

American (AMR)

AF:

0.504

AC:

7703

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

2042

AN:

3470

East Asian (EAS)

AF:

0.155

AC:

802

AN:

5162

South Asian (SAS)

AF:

0.529

AC:

2552

AN:

4824

European-Finnish (FIN)

AF:

0.493

AC:

5223

AN:

10584

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.554

AC:

37686

AN:

67964

Other (OTH)

AF:

0.549

AC:

1160

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2001

4002

6004

8005

10006

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

700

1400

2100

2800

3500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.538

Hom.:

5134

Bravo

AF:

0.517

Asia WGS

AF:

0.348

AC:

1216

AN:

3478

EpiCase

AF:

0.557

EpiControl

AF:

0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

4.0

PromoterAI

-0.098

Neutral

(source)

Mutation Taster

=297/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over